Gene loci information

Transcript annotation

  • This transcript has been annotated as Sodium-dependent nutrient amino acid transporter 1.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_3 g683 g683.t2 TSS g683.t2 5240282 5240282
chr_3 g683 g683.t2 isoform g683.t2 5240802 5243129
chr_3 g683 g683.t2 exon g683.t2.exon1 5240802 5240994
chr_3 g683 g683.t2 cds g683.t2.CDS1 5240802 5240994
chr_3 g683 g683.t2 exon g683.t2.exon2 5241161 5241223
chr_3 g683 g683.t2 cds g683.t2.CDS2 5241161 5241223
chr_3 g683 g683.t2 exon g683.t2.exon3 5241327 5241401
chr_3 g683 g683.t2 cds g683.t2.CDS3 5241327 5241401
chr_3 g683 g683.t2 exon g683.t2.exon4 5241585 5241641
chr_3 g683 g683.t2 cds g683.t2.CDS4 5241585 5241641
chr_3 g683 g683.t2 exon g683.t2.exon5 5241694 5242208
chr_3 g683 g683.t2 cds g683.t2.CDS5 5241694 5242208
chr_3 g683 g683.t2 exon g683.t2.exon6 5242268 5242424
chr_3 g683 g683.t2 cds g683.t2.CDS6 5242268 5242273
chr_3 g683 g683.t2 exon g683.t2.exon7 5242475 5242690
chr_3 g683 g683.t2 exon g683.t2.exon8 5242755 5243129
chr_3 g683 g683.t2 TTS g683.t2 NA NA

Sequences

>g683.t2 Gene=g683 Length=1651
ATGACTCAAGAAATTTACGACAATCCAGCATTTTCATCTGAAAATTCATTGTCTGTAATT
GAAGGAAATTTAACATCTGTGAATAATGAAGATAAAAATGAAGATCGAAAAATTGTCACA
AAAGATGGTGTTATTCGACAAAAATGGGGAAGAGATATAGAATTTCTTTTATCATGCATA
GCTATGGCCATAGTTGTAATTATTCAATCTTATATTTTTAGGAGGTTTCCTTTTATTGCC
TTGGAAAATGGAGGAGGTGCTTTTGTTATTCCATATATTATTGTACTAATTTTAATTGGA
AAACCTGGTTATTATTTGGAAATGATTATGGGCCAATTTTCTTCACGTGGCACAGTTAAA
GTTTATGATTGTGTTCCAGCTATGAGAGGTGTTGGATTAGGTCAAATGATTTGCCTTGCA
ATGGTTGCAACTTATTATTCAGCAATTGTTGCCATCATATTATATTTCCTTATCGTTTCT
TTTTTTCCTACTCTGCCATGGAGTGAATGCAAAGATTATTGGGATGTTCCATGCTATTCA
TCAAGTGGCAGCAACTCAAATATCACTTGGAATAATAACACAAAATCATCTGCGGAACTT
TATTTTTTAAAAGACGTTCTTAATGCTAGAGATACACTTGAAGATGGAATTGGTTTACCA
AATTGGAATTTAGTTGGACTTTTGGTTTTTTCATGGACAATAATGTTTATTCTTCTTTTT
AAAGGAGTGAGAATTACTGGAAAAGCTTCCTATGTCACAGGAACAGCTCCATTTATTTTT
CTAGCAATTTTTTTTATTCGAGCTATCACACTTGAGGGCTCATATGAAGGAATTGCTTAT
TTTTTCAAACCAAAATGGAATGATATTTTGAAGCCAAAAGTTTGGTTTGAAGCTTGCACT
CAAATTTGAACATAAAATACAACGTGATTCAGCTATTGTTACAACATTAGACACATTTAC
ATCACTTCTTGTTGGTTCGATTACCTTTGGTATTGTTGGTCATTTATCACATGAACTTAA
TAGACCAATTAAAGAGGTTTTCAGAGGAGGTCCTGGCTTGGTATTTGTCACTTATCCTGA
AACGATAGCAAAATTTAAATTTTGGCCACAATTCTTTTCTGTAATGTTTTTCCTGATGCT
TTTTATTCTTTCATTTGGAAGTTTACTTGCAACTTCATTATCGGCAATGACAGTAATTCG
CGATCGATTTAAAAGAATTAAAGATTGGCAAGCTGCTCTTGGATTTGCCATTTTTGGAAC
TATTTTTGGATGTTTTGCCGGATTGTTGATTCTTAATTTAGTCGACAGCTATTGTGCAAC
TTTTGTAATTTTTATCTTAGCCTGTCTTGAAATTTACACATTCTCCTATATTTATGGAGT
TGCCAGAATTTGTAAAGATGTAAAATTTATGCTGGGTTTCAGACCAAATATTTTTTGGAG
AGTAACTTGGAAATTTATAACACCACTTATTATGACAGCAATTGTTATTTACACATTTGT
ATATTTTGAACTTCCAAGTGATGGTGATTATCAATATCCAGTAGGAGCTCACATTTTTGG
TTGGTTTATAGCTTTATTAGGACTGATTTGGGTACCTGTAATTTTTACTACAAGAGTTTG
GAAACAAAAGCAAGAAACTAAATTGATTGAA

>g683.t2 Gene=g683 Length=302
MTQEIYDNPAFSSENSLSVIEGNLTSVNNEDKNEDRKIVTKDGVIRQKWGRDIEFLLSCI
AMAIVVIIQSYIFRRFPFIALENGGGAFVIPYIIVLILIGKPGYYLEMIMGQFSSRGTVK
VYDCVPAMRGVGLGQMICLAMVATYYSAIVAIILYFLIVSFFPTLPWSECKDYWDVPCYS
SSGSNSNITWNNNTKSSAELYFLKDVLNARDTLEDGIGLPNWNLVGLLVFSWTIMFILLF
KGVRITGKASYVTGTAPFIFLAIFFIRAITLEGSYEGIAYFFKPKWNDILKPKVWFEACT
QI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g683.t2 PANTHER PTHR11616 SODIUM/CHLORIDE DEPENDENT TRANSPORTER 21 302 4.2E-103
3 g683.t2 PANTHER PTHR11616:SF269 TRANSPORTER 21 302 4.2E-103
4 g683.t2 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 87 106 3.9E-15
5 g683.t2 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 130 156 3.9E-15
6 g683.t2 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 249 266 3.9E-15
1 g683.t2 Pfam PF00209 Sodium:neurotransmitter symporter family 46 302 1.2E-66
15 g683.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 54 -
24 g683.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 55 73 -
19 g683.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 74 84 -
23 g683.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 85 106 -
16 g683.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 107 136 -
22 g683.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 137 158 -
17 g683.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 159 221 -
21 g683.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 222 240 -
14 g683.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 241 251 -
20 g683.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 252 270 -
18 g683.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 271 302 -
13 g683.t2 ProSiteProfiles PS50267 Sodium:neurotransmitter symporter family profile. 45 302 34.525
12 g683.t2 SUPERFAMILY SSF161070 SNF-like 46 302 9.68E-66
7 g683.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 55 73 -
11 g683.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 78 100 -
10 g683.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 137 159 -
9 g683.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 218 240 -
8 g683.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 249 271 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0016021 integral component of membrane CC

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values